Comparative study of the binding and activation of 2,4-dichlorophenol by dehaloperoxidase A and B

Aktar, Mst Sharmin; Serrano, V.S. de; Ghiladi, Reza A.; Franzen, Stefan

doi:10.1016/j.jinorgbio.2023.112332

Cited by 4 publications

(16 citation statements)

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“…A previous enzyme kinetic study suggested that a lower heme and folding stability in DHP-B could be responsible for its higher catalytic efficiency due to a more dynamic structure enabling a higher substrate uptake . Dissociation constants for the important substrates 2,4-dichlorophenol and TCP are both 5 times smaller in DHP-B than in DHP-A …”

Section: Introductionmentioning

confidence: 95%

“…16,17 Based on kinetic assays of the peroxidase substrate 2,4,6-trichlorophenol (TCP), horseradish peroxidase (HRP) has a rate constant of k 1 ≈ 10 6 s −1 for the heterolytic cleavage of H 2 O 2 , while these rate constants are on the order of k 1 ≈ 10 4 s −1 for both DHP-A and DHP-B. 18,19 The rate constants in the peroxidase scheme are listed in Figure 2. The primary difference in activity between DHP-A and DHP-B is in the electron transfer rate constants, k 2 and k 3 .…”

Section: Introductionmentioning

confidence: 99%

“…17 Dissociation constants for the important substrates 2,4dichlorophenol and TCP are both 5 times smaller in DHP-B than in DHP-A. 18 Protein dynamic processes such as allostery, conformational changes, and catalytic turnover take place on a range of different time scales, anywhere from fs to hours and in some cases up to days or even longer. 35−45 Nuclear magnetic resonance (NMR) spectroscopy is a versatile technique that can provide information about a protein's structure and dynamic behavior at an atomic level over a wide range of time scales by measuring the relaxation rates of individual nuclei.…”

Section: Introductionmentioning

confidence: 99%

“…DHP has two isoforms, DHP-A and DHP-B (Figure ), which have a 96.4% sequence homology and differ only by five amino acids (I9L, R32K, Y34N, N81S, and S91G) . Although their backbones overlay almost perfectly and possess an almost identical protein fold, DHP-B has a 2- to 6-fold greater peroxidase activity chemistry depending on substrate, buffer, and pH. , Based on kinetic assays of the peroxidase substrate 2,4,6-trichlorophenol (TCP), horseradish peroxidase (HRP) has a rate constant of k 1 ≈ 10 6 s –1 for the heterolytic cleavage of H 2 O 2 , while these rate constants are on the order of k 1 ≈ 10 4 s –1 for both DHP-A and DHP-B. , The rate constants in the peroxidase scheme are listed in Figure . The primary difference in activity between DHP-A and DHP-B is in the electron transfer rate constants, k 2 and k 3 .…”

Section: Introductionmentioning

confidence: 99%

“…The site of substrate binding in solution is still in question and may differ substantially from the observed binding in crystals. While X-ray structures show substrates exclusively binding inside the distal pocket, there is evidence for the possibility of both internal and external binding occurring in solution. ,− We still do not know how much of the chemistry can occur for substrates internalized in the distal cavity of the globin, which is now identifiable as a substrate binding site. ,,− Various DHP mutants have been studied to probe the effects of electrostatics and dynamics on substrate binding. Electrostatic mutants that increase the negative charge on the surface of DHP-A have revealed a significant decrease in the rate for oxidation of TCP, which is also negatively charged at pH 7 .…”

Section: Introductionmentioning

confidence: 99%

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Comparison of the Backbone Dynamics of Dehaloperoxidase-Hemoglobin Isoenzymes

González-Delgado,

Thompson,

Andrałojć

et al. 2024

J. Phys. Chem. B

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Dehaloperoxidase (DHP) is a multifunctional hemeprotein with a functional switch generally regulated by the chemical class of the substrate. Its two isoforms, DHP-A and DHP-B, differ by only five amino acids and have an almost identical protein fold. However, the catalytic efficiency of DHP-B for oxidation by a peroxidase mechanism ranges from 2- to 6-fold greater than that of DHP-A depending on the conditions. X-ray crystallography has shown that many substrates and ligands have nearly identical binding in the two isoenzymes, suggesting that the difference in catalytic efficiency could be due to differences in the conformational dynamics. We compared the backbone dynamics of the DHP isoenzymes at pH 7 through heteronuclear relaxation dynamics at 11.75, 16.45, and 19.97 T in combination with four 300 ns MD simulations. While the overall dynamics of the isoenzymes are similar, there are specific local differences in functional regions of each protein. In DHP-A, Phe35 undergoes a slow chemical exchange between two conformational states likely coupled to a swinging motion of Tyr34. Moreover, Asn37 undergoes fast chemical exchange in DHP-A. Given that Phe35 and Asn37 are adjacent to Tyr34 and Tyr38, it is possible that their dynamics modulate the formation and migration of the active tyrosyl radicals in DHP-A at pH 7. Another significant difference is that both distal and proximal histidines have a 15–18% smaller S 2 value in DHP-B, thus their greater flexibility could account for the higher catalytic activity. The distal histidine grants substrate access to the distal pocket. The greater flexibility of the proximal histidine could also accelerate H2O2 activation at the heme Fe by increased coupling of an amino acid charge relay to stabilize the ferryl Fe(IV) oxidation state in a Poulos-Kraut “push–pull”-type peroxidase mechanism.

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Section: Introductionmentioning

confidence: 95%